PDBsum entry 1fka

Ribosome

PDB id: 1fka

Contents

Protein chains

111 a.a.*

176 a.a.*

161 a.a. *

157 a.a. *

97 a.a. *

128 a.a. *

136 a.a. *

89 a.a.* *

70 a.a.* *

103 a.a.* *

77 a.a.* *

26 a.a.* *

88 a.a. *

84 a.a. *

50 a.a. *

73 a.a. *

95 a.a. *

DNA/RNA

Metals

WO2 ×7

* Residue conservation analysis

* C-alpha coords only

References listed in PDB file

Key reference

Title

Structure of functionally activated small ribosomal subunit at 3.3 angstroms resolution.

Authors

F.Schluenzen, A.Tocilj, R.Zarivach, J.Harms, M.Gluehmann, D.Janell, A.Bashan, H.Bartels, I.Agmon, F.Franceschi, A.Yonath.

Ref.

Cell, 2000, 102, 615-623. [DOI no: 10.1016/S0092-8674(00)00084-2]

PubMed id

11007480

Abstract

The small ribosomal subunit performs the decoding of genetic information during translation. The structure of that from Thermus thermophilus shows that the decoding center, which positions mRNA and three tRNAs, is constructed entirely of RNA. The entrance to the mRNA channel will encircle the message when a latch-like contact closes and contributes to processivity and fidelity. Extended RNA helical elements that run longitudinally through the body transmit structural changes, correlating events at the particle's far end with the cycle of mRNA translocation at the decoding region. 96% of the nucleotides were traced and the main fold of all proteins was determined. The latter are either peripheral or appear to serve as linkers. Some may assist the directionality of translocation.

Figure 1.
Figure 1. The Small Subunit and Its Electron Density Map(Left and center) A stereo representation of the full model described in this paper. RNA is shown in gold, using a ribbon backbone and simple lines for base pairs. The differently colored helical segments and loops are the proteins. The major subdivisions are labeled: H, head; B, body; S, shoulder; P, platform; N, nose; F, foot.In all figures, the head is at the top of the drawing and the foot at the bottom.These portions of Figure 1 Figure 2 Figure 3 were made with Ribbons ( [12]).(Right) Segments showing RNA (top and middle pannels) and proteins (bottom) of the MIRAS map at 3.3 Å resolution, with the model superimposed. Made with O ([32]).

Figure 3.
Figure 3. The Presumed mRNA Path(Left) A surface representation of the subunit, viewed from the side of the 50S subunit. The latch is circled in cyan and the decoding center in red. The mRNA would enter the path in the approximate direction shown by the dark-blue arrow, pass through the aperture defined by the latch, and along the channel in the near face of the subunit. The brown curved arrows show the suggested global cooperative movements of the platform and the head, which facilitate the mRNA entrance, progression, and exit.(Right) Enlarged image of the decoding center region, showing the positions of tRNA anticodon stem loops and mRNA codons, using the superposition of tRNA and mRNA from the model of Cate et al., 1999, as described in the text. The uppermost bulge of H44 is shown in olive, two codons of mRNA in blue, and the anticodon bases of the tRNA molecules in green (A site), magenta (P site) and gray (E site). The right side of the figure was made with DINO ([47]). The contour level is 1.1 standard deviations.

The above figures are reprinted by permission from Cell Press: Cell (2000, 102, 615-623) copyright 2000.

Secondary reference #1

Title

Refining the overall structure and subdomain orientation of ribosomal protein s4 delta41 with dipolar couplings measured by nmr in uniaxial liquid crystalline phases.

Authors

M.A.Markus, R.B.Gerstner, D.E.Draper, D.A.Torchia.

Ref.

J Mol Biol, 1999, 292, 375-387. [DOI no: 10.1006/jmbi.1999.3061]

PubMed id

10493882

Figure 1.
Figure 1. Ribbon diagrams for (a) a representative structure from the original NMR ensemble of S4 delta41 and (b) the 1.7 Å crystal structure. In (a) and (b) the sheet- containing subdomain is in the same orientation, to emphasize both the similarity of the sheet- containing subdomains and the difference in the relative orien- tations of the helical subdomains. Elements of secondary structure and the chain termini are labeled. This Figure was generated with MOLSCRIPT (Kraulis, 1991).

Figure 5.
Figure 5. Stereoview of the sol- ution structure of S4 delta41, based on the NOE, hydrogen bond, dihedral angle, and N-H dipolar coupling restraints summarized in Table 1. The best 16 structures out of a cal- culation of 50 are shown in blue. For comparison, the crystal struc- ture is shown in magenta and the solution structure based on the original restraint list, lacking dipo- lar couplings, is shown in black. All structures are aligned by the backbone atoms in residues 94 to 176 (the sheet-containing subdo- main). Some residues at the ends of elements of secondary structure and the ends of the chain are labeled for reference.

The above figures are reproduced from the cited reference with permission from Elsevier

Secondary reference #2

Title

The structure of ribosomal protein s5 reveals sites of interaction with 16s rrna.

Authors

V.Ramakrishnan, S.W.White.

Ref.

Nature, 1992, 358, 768-771.

PubMed id

1508272

Secondary reference #3

Title

Crystal structure of the ribosomal protein s6 from thermus thermophilus.

Authors

M.Lindahl, L.A.Svensson, A.Liljas, S.E.Sedelnikova, I.A.Eliseikina, N.P.Fomenkova, N.Nevskaya, S.V.Nikonov, M.B.Garber, T.A.Muranova.

Ref.

Embo J, 1994, 13, 1249-1254.

PubMed id

8137808

Secondary reference #4

Title

The structure of ribosomal protein s7 at 1.9 a resolution reveals a beta-Hairpin motif that binds double-Stranded nucleic acids.

Authors

B.T.Wimberly, S.W.White, V.Ramakrishnan.

Ref.

Structure, 1997, 5, 1187-1198. [DOI no: 10.1016/S0969-2126(97)00269-4]

PubMed id

9331418

Figure 4.
Figure 4. RNA-binding regions of S7. (a) Electrostatic surface potential of S7. The potential displayed represents a range from -12 to +12 k[B]T, shown with red as negative and blue as positive. The surface potential calculation and display was done using the program GRASP [84]. (b) Ribbon diagram of a similar view, showing residues that are likely to be involved in RNA-binding. Basic residues are shown in blue and solvent-exposed hydrophobic residues are shown in yellow. The red residues R76 and A116 correspond to the sites of crosslinks to 16S RNA. The figure was produced using the program MOLSCRIPT [82].

The above figure is reproduced from the cited reference with permission from Cell Press

Secondary reference #5

Title

Crystal structure of ribosomal protein s8 from thermus thermophilus reveals a high degree of structural conservation of a specific RNA binding site.

Authors

N.Nevskaya, S.Tishchenko, A.Nikulin, S.Al-Karadaghi, A.Liljas, B.Ehresmann, C.Ehresmann, M.Garber, S.Nikonov.

Ref.

J Mol Biol, 1998, 279, 233-244. [DOI no: 10.1006/jmbi.1998.1758]

PubMed id

9636713

Figure 2.
Figure 2. Schematic representation of the structure of ribosomal protein S8 from T. thermophilus. The Figure was made using MOLSCRIPT (Kraulis, 1991).

The above figure is reproduced from the cited reference with permission from Elsevier

Secondary reference #6

Title

Conformational variability of the n-Terminal helix in the structure of ribosomal protein s15.

Authors

W.M.Clemons, C.Davies, S.W.White, V.Ramakrishnan.

Ref.

Structure, 1998, 6, 429-438. [DOI no: 10.1016/S0969-2126(98)00045-8]

PubMed id

9562554

Figure 2.
Figure 2. Overall fold of S15. (a) Stereo view ribbon diagram of S15 with the alternate conformation of the N-terminal helix shown in dark gray. (b) Stereo view Cα trace in the same view as (a) with every tenth residue shown as a small black sphere and labeled; the alternate conformation of the helix is shown in white. (The figures were made using the program MOLSCRIPT [46].)

The above figure is reproduced from the cited reference with permission from Cell Press

Secondary reference #7

Title

Structure of the s15,S6,S18-Rrna complex: assembly of the 30s ribosome central domain.

Authors

S.C.Agalarov, G.Sridhar prasad, P.M.Funke, C.D.Stout, J.R.Williamson.

Ref.

Science, 2000, 288, 107-113. [DOI no: 10.1126/science.288.5463.107]

PubMed id

10753109

Figure 4.
Fig. 4. Details of S15-Tth T4 RNA interactions. Bases and side chains are rendered as thick sticks, riboses as thin sticks, groups involved in interactions are colored by atom. (A) S15 interactions with the helix 20, 21, 22 junction. Nucleotides U652, G654, G752, A753, and C754 in the junction are blue. The OH group of the highly conserved Tyr68 contacts G752 O3', while the side-chain ring packs tightly against C754. S15 residues in the 1- 2 loop make direct minor groove contacts in helix 22, including Asp20 to G750 O2'; Thr21 to G657 N2 and O2'; Gly22 backbone N and O to G750 O2' and N2, respectively; Thr24 to U751 O2'; and Gln27 to C656 O2 and O2' and to G750 N2. (B) S15 interactions with the helix 22 purine-rich loop. Residue His41 stacks under His45, forms a hydrogen bond with Asp48, and contacts C739 O2', while His45 contacts G668 N2. Residue Asp48 interacts with Ser51 and contacts G667 N2 and O2', while Ser51 makes contacts to U740 O2 and O2', and to G666 N2. (C) S15 interaction with the helix 23a GAAG tetraloop. Nucleotide A665 from helix 22 is in green, all bases in helix 23a are in pink. Residue His50 from 3 contacts A728 N6, A729 N6, and G730 O6, while conserved residue Arg53 stacks below the purine ring of A728. Figure created with InsightII.

Figure 5.
Fig. 5. Details of S6:S18-Tth T4 RNA interaction. Molecules are rendered and colored as in Fig. 4, with phosphate groups shown as spheres. S6 residues located near the NH[2]-terminus, in 2, and in 4 make electrostatic and hydrogen-bonding contacts to the Tth T4 RNA in the minor groove between helix 22 and helix 23b. These contacts include Arg2, Tyr4, and Lys92 to A737 and C738 phosphates, Arg87 to G673 phosphate and O3', Val90 carbonyl oxygen to C736 O2', and Asn73 to G670 N2 and A737 N3. The charged S18 residues Lys68, Lys71, and Arg72, from the COOH-terminal end of the helix, contact the phosphate groups of C735, C736, and A737 in helix 22 near the upper three-helix junction. Residue Arg64, which is located near the other end of the S18 helix, contacts the G664 phosphate located across the narrowed major groove of helix 22 near the interhelical A665:G724 base pair. Residues Lys71 and Arg74 also make four base-specific contacts to the single-stranded nucleotides C719, C720, and G721 in helix 23a. Figure created with InsightII.

The above figures are reproduced from the cited reference with permission from the AAAs

Secondary reference #8

Title

Solution structure of the ribosomal protein s19 from thermus thermophilus.

Authors

M.Helgstrand, A.V.Rak, P.Allard, N.Davydova, M.B.Garber, T.Härd.

Ref.

J Mol Biol, 1999, 292, 1071-1081. [DOI no: 10.1006/jmbi.1999.3122]

PubMed id

10512703

Figure 3.
Figure 3. (a) Stereo view of the superimposed backbones (residues Gly8 to Tyr80) of the 21 structures in angle bracket SA angle bracket . (b) MOLMOL representation of the secondary structure elements of S19.

Figure 6.
Figure 6. Two potential interaction sites in S19. The side-chains of residues Trp34-Ser35-Arg36-Arg37-Ser38 are shown in red and those in the fragment Val67 to Thr77 are shown in green (see the text for a further discussion).

The above figures are reproduced from the cited reference with permission from Elsevier